This is one of the discussions that comes up over and over again. I’m in the camp that says you can use flurry of blows and Two-Weapon Fighting at the same time. Not everybody is. My take on it is:
Flurry of blows adds one attack at your highest attack bonus when you use it. You can only use it when using a monk weapon as your primary attack (the one that you use your normal iterative attacks on.) Unarmed strike is the normal weapon a monk uses this way, and represents all of your body parts that you can smack things with. When you use flurry of blows, you take a −2 penalty to all attacks that round. (At higher levels, that penalty is reduced, and later a third attack at the highest attack bonus is gained.)
Two-weapon fighting adds an extra attack with the off-hand. If you do two-weapon fighting with the two-weapon fighting feat and unarmed attack for the off-hand attack, you’ll take a −2 penalty on all attacks that round.
So a first level monk with the Two-Weapon Fighting feat who chose to use flurry of blows and two-weapon fighting at the same time would get three attacks, at −4/−4 for the main attack, and −4 for the off-hand attack. An ninth-level monk who has additionally taken Improved Two-Weapon Fighting would get main-hand attacks at −2/−2/−7, and off-hand attacks at −2/−7. (At level 9, the flurry penalty has been gone for some time.) At fifteenth level, if the monk has Greater Two-Weapon Fighting, the monk would get main-hand attacks at −2/−2/−2/−7/−12, and off-hand attacks at −2/−7/−12. (This is with greater flurry, gaining a third flurry attack at level 11.)
In this model, a fully tricked-out TWF monk would have (adding in the BAB now, instead of just giving the penalties of each attack) attacks at +13/+13/+13/+8/+3 main hand, and +13/+8/+3 off-hand. Which is a whole heck of a lot of attacks.
The pinnacle of ridiculous melee attacks is the fighter 4/monk 16, who gets attacks at +14/+14/+14/+9/+4/−1 with the main hand, and +14/+9/+4 with the off-hand (and has the option of taking the Perfect Two-Weapon Fighting epic feat. Which... could work in a number of contradictory ways.
In any case, the key here is that you take penalties from flurry and penalties from TWF, and penalties always always stack. But the flurry penalties go away.
For combining flurry of blows and Rapid Shot, it’s the same thing. −4/−4/−4 for attacks with shuriken at level 1. This is easier than the TWF stuff, because there’s no way to get iterative attacks by chaining more feats on top of Rapid Shot. So at level 20, a pure monk would be at +13/+13/+13/+13/+7/+3 to attack with shuriken using flurry of blows and Rapid Shot.
P.S. If you decide to make such a character, remember two things: 1) taking a −4 penalty on attack rolls at level 1 is a bit much: better to wait until your flurry penalty is reduced, and 2) bring a lot of dice so you don’t waste time having to do each attack roll one after another.
